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Catechol O-methyltransferase from Streptomyces avermitilis in complex with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2M Ammonium formate, 10% w/v Polyvinylpyrrolidone 20% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.07 40.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.398 α = 90 b = 41.596 β = 96.564 c = 104.207 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2022-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 46.09 99.2 0.158 0.998 9.2 7.6 36681
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 1.406 0.603
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 46.09 36669 1855 99.036 0.164 0.162 0.2107 0.2024 22.338
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.127 -0.492 0.571 0.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.761 r_dihedral_angle_4_deg 17.719 r_dihedral_angle_3_deg 13.534 r_dihedral_angle_1_deg 5.829 r_lrange_it 5.098 r_lrange_other 5.06 r_scangle_it 4.268 r_scangle_other 4.267 r_scbond_it 2.773 r_scbond_other 2.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.761 r_dihedral_angle_4_deg 17.719 r_dihedral_angle_3_deg 13.534 r_dihedral_angle_1_deg 5.829 r_lrange_it 5.098 r_lrange_other 5.06 r_scangle_it 4.268 r_scangle_other 4.267 r_scbond_it 2.773 r_scbond_other 2.773 r_mcangle_it 2.154 r_mcangle_other 2.153 r_mcbond_it 1.561 r_mcbond_other 1.561 r_angle_refined_deg 1.528 r_angle_other_deg 1.375 r_nbd_other 0.247 r_symmetry_nbd_refined 0.209 r_nbd_refined 0.201 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.182 r_symmetry_xyhbond_nbd_other 0.165 r_nbtor_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3388 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building MOLREP phasing